I have to admit after working with the concept for awhile, that
for proofing, numbered words does has some use, especially in
clarity. For instance, may I propose a shorthand? Something like

2r.8.8 <ee>=<e,e> or
2r.8.8 {C}={c,c}.

This would be short for "At Folio 2r, line 8, word 8, you have EVA
<ee> written as one glyph (also written as VGBT {C} ), when I
think this should be EVA <e,e> as two glyphs, (which can also be
written as VGBT {c,c}.)

Either proofing language works as long as they're identified with
<> for EVA and {} for VGBT, although I expect we'll probably be
using EVA for most of the discussion. This might be a good way of
submitting long lists of proofing corrections and an easy way to
maintain them in a list for comparison?

If you make the web-page more "live" (ie, make the word index into a
hyper-link to an HTML form), all this becomes rather secondary (as the
form's submit-button JavaScript can trivially handle all the proofing
formatting you're describing). I'll mock up an example of this to show what
I mean.

Still, having a unique page/line/word index would almost certainly be
useful, if only for identifying interesting words in the document that we
might perhaps want to debate on-list. :-)